Simulation setup
First, import pyrid
import pyrid as prd
The user ‘communicates’ with PyRID via the Simulation class. To configure a simulation system in PyRID, some parameters need to be defined by the user. These include the
simulation box size (in nm),
integration time step (in ns),
temperature (in Kelvin),
solvent viscosity (in kJ/(nm^3 ns)),
number of simulation steps,
Then, a simulation can be set up by:
Simulation = prd.Simulation(box_lengths = [50.0,50.0,50.0],
dt = 0.1,
Temp = 293.15,
eta = 1e-21,
nsteps = 1e5)
By default, energy is given in units of kJ/mol, length in nanometer and time in ns. The user can, however, define different units such as micrometer and s.
Simulation = prd.Simulation(box_lengths = [50.0,50.0,50.0],
dt = 0.1,
Temp = 293.15,
eta = 1e-21,
nsteps = 1e5,
length_unit = 'nanometer',
time_unit = 'ns')
In addition, there are many other parameters the user can define. For example the directories for files and figures:
Simulation = prd.Simulation(box_lengths = [50.0,50.0,50.0],
dt = 0.1,
Temp = 293.15,
eta = 1e-21,
nsteps = 1e5,
length_unit = 'nanometer',
time_unit = 'ns',
file_path = 'my_directory/',
fig_path = 'Figures/',
file_name='my_first_simulation')
By default, PyRID writes the molecule trajectories into a .xyz file with a stride of 100. You may change these settings:
Simulation = prd.Simulation(box_lengths = [50.0,50.0,50.0],
dt = 0.1,
Temp = 293.15,
eta = 1e-21,
nsteps = 1e5,
length_unit = 'nanometer',
time_unit = 'ns',
file_path = 'my_directory/',
fig_path = 'Figures/',
file_name='my_first_simulation',
write_trajectory = True,
stride = 100)
ALso, the user can set a random seed. Thereby, a simulation will be exactly reproducible:
Simulation = prd.Simulation(box_lengths = [50.0,50.0,50.0],
dt = 0.1,
Temp = 293.15,
eta = 1e-21,
nsteps = 1e5,
length_unit = 'nanometer',
time_unit = 'ns',
file_path = 'my_directory/',
fig_path = 'Figures/',
file_name='my_first_simulation',
write_trajectory = True,
stride = 100,
seed = 0)
PyRID supports three different types of boundary conditions: ‘periodic’, ‘repulsive’, ‘fixed concentration’. By default, PyRID assumes periodic boundary conditions. If you want to use repulsive boundary conditions, you can set a wall_force constant. By default wall_force = 100. The same constant is also used to resolve collisions of molecules with mesh compartment walls.
Simulation = prd.Simulation(box_lengths = [50.0,50.0,50.0],
dt = 0.1,
Temp = 293.15,
eta = 1e-21,
nsteps = 1e5,
length_unit = 'nanometer',
time_unit = 'ns',
file_path = 'my_directory/',
fig_path = 'Figures/',
file_name='my_first_simulation',
write_trajectory = True,
stride = 100,
seed = 0,
boundary_condition = 'repulsive',
wall_force = 100.0)
Sometimes you may don’t want to specify the number of time steps but rather limit the total simulation time. In this case, you can pass sim_time (given in seconds, e.g. 7200 s for a 2 hour simulation) instead of nsteps:
Simulation = prd.Simulation(box_lengths = [50.0,50.0,50.0],
dt = 0.1,
Temp = 293.15,
eta = 1e-21,
sim_time = 7200)
Once an instance of the Simulation class is created we may continue configuring our simulation. For long simulations, it is often convenient to add checkpoints, i.e. PyRID saves the state of the system at certain points. checkpoints are saved in numpy .npz files. You can add checkpoints by:
Simulation.add_checkpoints(1000, "checkpoints/", 10)
Here, 1000 sets the stride, i.e. PyRID will save the System state each 100th step, “checkpoints/” is the directory, and 10 sets the maximum number of saved files. If you want to load a checkpoint, you can do so by
Simulation.load_checkpoint('my_first_simulation', 0)
, where ‘my_first_simulation’ is the file name and 0 the index of the saved file. In our example there are 10 saved files with indices 0-9. Note that PyRID currently does not save the complete system configuration. That mean, all the molecule types, particles, interactions and reactions need to be declared again, before you can load a checkpoint file. For future releases it would, however, be nice to be able to save complete project files which can then be loaded. In the next chapter you learn how to add molecules to the system.
Berendsen barostat
PyRID also supports NPT ensemble simulations using a Berendsen barostat. A barostat can be setup as follows:
P0 = 0.0 # target pressure
Tau_P= 1.0 # time constant
start = 10000 # time step at which to start the barostat
Simulation.add_barostat_berendsen(Tau_P, P0, start)